The fuel cell system is environment-friendly and energy efficient system. Especially, the fuel cell cogeneration systems providing heat and electricity to buildings have been developed and applied to a lot of sites in the world to cope with the global warming and $CO_2$ emission problem. This paper presents the result of study on the economic evaluation with super-micro fuel cell (SMFC) cogeneration system by varying the floor area ($132m^2{sim}331m^2$) of the house, whose system capacity ranges from 0.10 kWe to 0.50 kWe. The electricity demand, heat demand, saved energy cost, and the simple pay-back period have been simulated for the various capacities of fuel cell cogeneration system. As a result, this study suggests the fuel cell system’s capacity decision strategy for a given house area. Contrary to conventional design assumptions, the smaller capacity fuel cell cogeneration system is appropriate for the house of large floor area to defense the progressive electricity tax, and the larger capacity fuel cell cogeneration system is appropriate for the house of small floor area to sell the electricity.